SMTL ID : 6epk.1 (1 other biounit)

CRYSTAL STRUCTURE OF THE PRECURSOR MEMBRANE PROTEIN-ENVELOPE PROTEIN HETERODIMER FROM THE YELLOW FEVER VIRUS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain B: K.6, L.11, N.13, W.40 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.2: 7 residues within 4Å: Chain B: T.22, N.29, P.54, R.55, E.56, E.57, Y.66 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.54, B:R.55, B:R.55, B:R.55

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: F.172, T.173, G.174, G.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.174, A:G.176 SO4.4: 4 residues within 4Å: Chain A: E.227, M.228, H.229 Ligands: GOL.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.227, A:M.228, A:H.229 Salt bridges: A:H.229 SO4.5: 2 residues within 4Å: Chain A: R.207, Q.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.211 Salt bridges: A:R.207 SO4.6: 3 residues within 4Å: Chain A: K.326, G.327, N.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.327, A:N.359 SO4.7: 3 residues within 4Å: Chain A: C.92, K.93, R.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 SO4.8: 2 residues within 4Å: Chain A: H.67 Chain B: P.42 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.67 Salt bridges: A:H.67 SO4.9: 5 residues within 4Å: Chain A: K.293, G.294, T.295, S.296, Y.297 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.294, A:T.295, A:T.295, A:S.296, A:S.296 SO4.10: 4 residues within 4Å: Chain A: K.93, T.95, P.236, P.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.95 Salt bridges: A:K.93 SO4.11: 2 residues within 4Å: Chain A: N.62, N.249 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.62, A:N.249 Water bridges: A:N.249 Salt bridges: A:K.123 SO4.17: 2 residues within 4Å: Chain A: K.73 Chain B: R.8 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.73, B:R.8 SO4.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 9 residues within 4Å: Chain A: A.1, H.144, V.145, G.146, A.147, W.152, T.351, L.364, E.366 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.146, A:A.147, A:A.147, A:E.366 GOL.13: 4 residues within 4Å: Chain A: D.339, L.340, T.341, Y.375 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.340, A:T.341 GOL.14: 3 residues within 4Å: Chain A: R.226, E.227 Ligands: SO4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.227 GOL.15: 5 residues within 4Å: Chain A: D.72, K.73, R.99, G.104 Chain B: N.51 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.72, A:R.99, B:N.48, B:N.51 Water bridges: A:C.74 GOL.16: 3 residues within 4Å: Chain A: H.238, R.243 Chain B: E.36 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.238, A:R.243, B:E.36, B:E.36 Water bridges: A:R.243 GOL.19: 2 residues within 4Å: Chain B: C.78, D.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.77 GOL.20: 1 residues within 4Å: Chain B: R.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crampon, E. et al., New insight into flavivirus maturation from structure/function studies of the yellow fever virus envelope protein complex. Mbio (2023)

Release Date

2018-10-31

Peptides

Envelope protein E: A
Precursor Membrane Protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Envelope protein E

Precursor Membrane Protein

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